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Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 0.1M TRIS pH 8, 0.2M Ammonium Sulfate, 30% PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.017 α = 90 b = 41.017 β = 90 c = 104.995 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F double crystal monochromator 2018-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.65 35.52 99.7 0.068 0.073 0.024 0.999 18.1 8.9 12894
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 95.3 0.803 0.86 0.302 0.899 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1rv1 1.8 35.52 9597 451 99.96 0.1364 0.1323 0.2257 0.2308 RANDOM 20.772
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.1 -0.05 -0.1 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.524 r_sphericity_free 30.52 r_sphericity_bonded 20.755 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_4_deg 14.776 r_dihedral_angle_1_deg 6.154 r_rigid_bond_restr 3.162 r_angle_refined_deg 1.993 r_angle_other_deg 0.957 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.524 r_sphericity_free 30.52 r_sphericity_bonded 20.755 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_4_deg 14.776 r_dihedral_angle_1_deg 6.154 r_rigid_bond_restr 3.162 r_angle_refined_deg 1.993 r_angle_other_deg 0.957 r_chiral_restr 0.095 r_bond_refined_d 0.025 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 823 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing